mcdr-mtb-standalone-v2

Introduction

mcdr-mtb-standalone-v2 is a pipeline for prediction of drug resistance class (MDR, Pre-XDR, XDR or Susceptible) of Mycobacterium tuberculosis isolates from whole genome sequencing (WGS) data. The users can start with paired-end FASTQ files or variant calling output VCF files.

• Workflows
• Pre-requisites
• Installation
• Usage
  • 1. Prediction of drug resistance class of one or many MTB paired-end FASTQ files
  • 2. Prediction of drug resistance class of a single MTB VCF file
  • 3. Prediction of drug resistance class of multiple MTB VCF files
  • 4. Prediction of drug resistance class of merged MTB VCF file
• Demo runs
  • 1. Prediction from FASTQ (Single isolate)
  • 2. Prediction from FASTQ (Multiple isolates)
  • 3. Prediction from single VCF
  • 4. Prediction from multiple VCFs
  • 5. Prediction from merged VCFs
• Team
• Disclaimer

Workflows

There are 4 different scripts for prediction:

• mcdr-WGS-predict.sh: Prediction of drug resistance class of single or multiple MTB WGS data (paired-end fastq files).
• mcdr-VCF-predict.sh: Prediction of drug resistance class of single MTB VCF file.
• mcdr-multi-VCF-predict.sh: Prediction of drug resistance class of multiple MTB VCF files.
• mcdr-merge-VCF-predict.sh: Prediction of drug resistance class of MTB merged VCF file.

Pre-requisites

• trim-galore (version 0.6.7) - quality check and trimming of read sequences
• bwa (version 0.7.17-r1188) - reference based alignment
• samtools (version 1.13)- processing the BAM files
• freebayes (version v1.3.6) - variant calling
• libvcflib-tools (version 1.0.7) - processing the VCF files
• libvcflib-dev (version 1.0.7) - processing the VCF files
• bgzip (version 1.13+ds) - zipping files
• R (version 4.2.2 Patched (2022-11-10 r83330)) - data operation and machine learning model usage

Installation

Step 1: Install dependent packages/tools

(For ubuntu)

sudo apt-get install trim-galore bwa samtools freebayes libvcflib-tools libvcflib-dev bgzip

(For other distributions)

The installation steps for the different packages/tools are given in the following links:

• trim-galore - https://github.com/FelixKrueger/TrimGalore
• bwa - https://github.com/lh3/bwa
• samtools, bcftools, bgzip(htstools) - http://www.htslib.org/download/
• freebayes - https://github.com/freebayes/freebayes
• vcflib - https://github.com/vcflib/vcflib

R should be installed in the user system/PC. R installation steps are given in https://cran.r-project.org/. The following R packages are required for the prediction of drug resistance class:

install.packages("caret")
install.packages("reshape2")
install.packages("ggplot2")
install.packages("DALEX")
install.packages("RSNNS")

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Step 2: Install mcdr-mtb-standalone-v2

I. Download the software from GitHub repository

Create a clone of the repository:

  git clone https://github.com/PulmonomicsLab/mcdr-mtb-standalone-v2

Note: Creating a clone of the repository requires git to be installed.

The git can be installed using

  sudo apt-get install git

OR

Download using wget:

  wget https://github.com/PulmonomicsLab/mcdr-mtb-standalone-v2/archive/refs/heads/main.zip
  unzip main.zip

Note: wget can be installed using

  sudo apt-get install wget

II. Make the shell scripts executable

chmod +x INSTALLATION_DIR/mcdr-mtb-standalone-v2/config.sh
chmod +x INSTALLATION_DIR/mcdr-mtb-standalone-v2/mcdr-WGS-predict.sh
chmod +x INSTALLATION_DIR/mcdr-mtb-standalone-v2/mcdr-VCF-predict.sh
chmod +x INSTALLATION_DIR/mcdr-mtb-standalone-v2/mcdr-multi-VCF-predict.sh
chmod +x INSTALLATION_DIR/mcdr-mtb-standalone-v2/mcdr-merge-VCF-predict.sh

INSTALLATION_DIR = Directory where mcdr-mtb-standalone-v2 is installed

III. update the paths in config.sh (optional)

The config.sh looks like

freebayes_path=/usr/bin/freebayes
samtools_path=/usr/bin/samtools
bwa_path=/usr/bin/bwa
trim_galore_path=/usr/bin/trim_galore
vcflib_path=/usr/bin/vcflib
bgzip_path=/usr/bin/bgzip
bcftools_path=/usr/bin/bcftools
trim_galore_cores=4
bwa_mem_cores=4
samtools_cores=4

Note: It shows the default paths of the executables files for freebayes, samtools, bwa, trim galore!, vcflib, bgzip and bcftools. The users need to update the paths of the executables, in case these tools were installed in ways other than the apt-get install command.

Usage

Initially change the directory to the directory where mcdr-mtb-standalone-v2 is installed.

cd INSTALLATION_DIR/mcdr-mtb-standalone-v2

Different operations can be performed by calling the appropriate scripts with two command-line arguments: INPUT_DIR and OUTPUT_DIR.

INPUT_DIR = the path (absolute or relative) of the folder containing the input files.

OUTPUT_DIR = the path (absolute or relative) of the folder in which mcdr-mtb-standalone-v2 will store the outputs.

The executable script, and contents of INPUT_DIR and OUTPUT_DIR depends on the choice of operations. The different operations are explained below.

1. Prediction of drug resistance class of one or many MTB paired-end FASTQ files

(.fastq to drug resistance class (S, M, P, X))

./mcdr-WGS-predict.sh INPUT_DIR OUTPUT_DIR

INPUT_DIR must contain paired end FASTQ (<sample_id>_1.fastq.gz & <sample_id>_2.fastq.gz) of 1 or more isolates.

OUTPUT_DIR will contain

• one folder for each ISOLATE ID. Each folder will contain
  • the VCF file (<sample_id>.vcf)
  • the intermediate BAM files (<sample_id>.bam, <sample_id>_sorted.bam)
• the MERGED.vcf file (only in case of multiple isolates)
• the intermediate TSV file (<sample_id>.tsv/MERGED.tsv)
• the prediction result performed with the full model (prediction.tsv)
• the SHAP result for each isolate with the 37-feature model (shap_result_37_features_<sample_id>.tsv)
• the SHAP result for each isolate with the 100-feature model (shap_result_100_features_<sample_id>.tsv)
• the SHAP result plot for each isolate with the 37-feature model (shap_plot_37_features_<sample_id>.svg)
• the SHAP result plot for each isolate with the 100-feature model (shap_plot_100_features_<sample_id>.svg)

Note: The merged.vcf file will not be present if there was only one isolate in the INPUT_DIR.
The prediction and the SHAP results output will also be displayed on the terminal.

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2. Prediction of drug resistance class of a single MTB VCF file

(.vcf to drug resistance class (S, M, P, X))

./mcdr-VCF-predict.sh INPUT_DIR OUTPUT_DIR

INPUT_DIR must contain VCF file (<sample_id>.vcf)

OUTPUT_DIR will contain

• intermediate .tsv file (<sample_id>.tsv)
• the prediction result performed with the full model (prediction.tsv)
• the SHAP result for the isolate with the 37-feature model (shap_result_37_features_<sample_id>.tsv)
• the SHAP result for the isolate with the 100-feature model (shap_result_100_features_<sample_id>.tsv)
• the SHAP result plot for the isolate with the 37-feature model (shap_plot_37_features_<sample_id>.svg)
• the SHAP result plot for the isolate with the 100-feature model (shap_plot_100_features_<sample_id>.svg)

The prediction and the SHAP results output will also be displayed on the terminal.

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3. Prediction of drug resistance class of multiple MTB VCF files

(multiple .vcf to drug resistance class (S, M, P, X))

./mcdr-multi-VCF-predict.sh INPUT_DIR OUTPUT_DIR

INPUT_DIR must contain more than 1 VCF file (<sample_id_1>.vcf, <sample_id_2>.vcf, … , <sample_id_n>.vcf)

OUTPUT_DIR will contain

• the MERGED.vcf file
• the intermediate .tsv file (MERGED.tsv)
• the prediction result performed with the full model (prediction.tsv)
• the SHAP result for each isolate with the 37-feature model (shap_result_37_features_<sample_id>.tsv)
• the SHAP result for each isolate with the 100-feature model (shap_result_100_features_<sample_id>.tsv)
• the SHAP result plot for each isolate with the 37-feature model (shap_plot_37_features_<sample_id>.svg)
• the SHAP result plot for each isolate with the 100-feature model (shap_plot_100_features_<sample_id>.svg)

The prediction and the SHAP results output will also be displayed on the terminal.

---

4. Prediction of drug resistance class of merged MTB VCF file

(merged.vcf to drug resistance class (S, M, P, X))

./mcdr-merge-VCF-predict.sh INPUT_DIR OUTPUT_DIR

INPUT_DIR must contain a merged VCF file (MERGED.vcf) with information of one or more isolates.

OUTPUT_DIR will contain

• the intermediate .tsv file (MERGED.tsv)
• the prediction result performed with the full model (prediction.tsv)
• the SHAP result for each isolate with the 37-feature model (shap_result_37_features_<sample_id>.tsv)
• the SHAP result for each isolate with the 100-feature model (shap_result_100_features_<sample_id>.tsv)
• the SHAP result plot for each isolate with the 37-feature model (shap_plot_37_features_<sample_id>.svg)
• the SHAP result plot for each isolate with the 100-feature model (shap_plot_100_features_<sample_id>.svg)

The prediction and the SHAP results output will also be displayed on the terminal.

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Demo runs

1. Prediction from FASTQ (Single isolate)

Step 1. Create an Input directory

   mkdir /home/username/Input_Dir1

Step 2. Get Data

Download the whole genome sequencing FASTQ files of a MTB isolate run, ERR137249 (ERR137249_1.fastq & ERR137249_2.fastq) from https://www.ebi.ac.uk/ena/browser/view/ERR137249

Step 3. Store these files in Input_Dir1

Step 4. Create an Output directory

   mkdir /home/username/Output_Dir1

Step 5. Go to the mcdr-mtb-standalone-v2 installation directory

   cd /home/username/mcdr-mtb-standalone-v2/

Step 6. Run mcdr-WGS-predict.sh

   ./mcdr-WGS-predict.sh /home/username/Input_Dir1/ /home/username/Output_Dir1/

Input_Dir1 contains ERR137249_1.fastq, ERR137249_2.fastq

Output_Dir1 contains -

• A folder - ERR137249 - which contains:
  • reference folder - reference genome and index files
  • Trim galore outputs - ERR137249_1_val_1.fq.gz, ERR137249_2_val_2.fq.gz, ERR137249_1_trimming_report.txt, ERR137249_2_trimming_report.txt
  • Bwa-mem output - ERR137249.bam
  • Intermediate BAM files - ERR137249_fix.bam, ERR137249_namesort.bam, ERR137249_positionsort.bam, ERR137249_markdup.bam
  • BAM index - ERR137249.bam.bai
  • Freebayes output - ERR137249.vcf
  • VCF compressed - ERR137249.vcf.gz
  • VCF index - ERR137249.vcf.gz.csi
• ERR137249.tsv - the intermediate TSV file
• prediction.tsv - the prediction result performed with the full model
• shap_result_37_features_ERR137249.tsv - the SHAP result for ERR137249 with the 37-feature model
• shap_result_100_features_ERR137249.tsv - the SHAP result for ERR137249 with the 100-feature model
• shap_plot_37_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 37-feature model
• shap_plot_100_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 100-feature model

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2. Prediction from FASTQ (Multiple isolates)

Step 1. Create an Input directory

mkdir /home/username/Input_Dir2

Step 2. Get Data

Download the whole genome sequencing FASTQ files of MTB ISOLATE runs, ERR137249 (ERR137249_1.fastq & ERR137249_2.fastq) and SRR1103491 (SRR1103491_1.fastq & SRR1103491_2.fastq) from https://www.ebi.ac.uk/ena/browser/view/ERR137249 and https://www.ebi.ac.uk/ena/browser/view/SRR1103491

Step 3. Store these files in Input_Dir2

Step 4. Create an Output directory

mkdir /home/username/Output_Dir2

Step 5. Go to the mcdr-mtb-standalone-v2 installation directory

cd /home/username/mcdr-mtb-standalone-v2/

Step 6. Run mcdr-WGS-predict.sh

./mcdr-WGS-predict.sh /home/username/Input_Dir1/ /home/username/Output_Dir2/

Input_Dir2 contains ERR137249_1.fastq, ERR137249_2.fastq, SRR1103491_1.fastq, SRR1103491_2.fastq

Output_Dir2 contains -

• Two folders - ERR137249, SRR1103491 - each containing:
  • reference folder - reference genome and index files
  • Trim galore outputs - ISOLATENAME_1_val_1.fq.gz, ISOLATENAME_2_val_2.fq.gz, ISOLATENAME_1_trimming_report.txt, ISOLATENAME_2_trimming_report.txt
  • Bwa-mem output - ISOLATENAME.bam
  • Intermediate BAM files - ISOLATENAME_fix.bam, ISOLATENAME_namesort.bam, ISOLATENAME_positionsort.bam, ISOLATENAME_markdup.bam
  • BAM index - ISOLATENAME.bam.bai
  • Freebayes output - ISOLATENAME.vcf
  • VCF compressed - ISOLATENAME.vcf.gz
  • VCF index - ISOLATENAME.vcf.gz.csi
• merged.vcf
• merged.tsv - the intermediate TSV file
• prediction.tsv - the prediction result performed with the full model
• shap_result_37_features_ERR137249.tsv - the SHAP result for ERR137249 with the 37-feature model
• shap_result_100_features_ERR137249.tsv - the SHAP result for ERR137249 with the 100-feature model
• shap_plot_37_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 37-feature model
• shap_plot_100_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 100-feature model
• shap_result_37_features_SRR1103491.tsv - the SHAP result for SRR1103491 with the 37-feature model
• shap_result_100_features_SRR1103491.tsv - the SHAP result for SRR1103491 with the 100-feature model
• shap_plot_37_features_SRR1103491.svg - the SHAP result plot for SRR1103491 with the 37-feature model
• shap_plot_100_features_SRR1103491.svg - the SHAP result plot for SRR1103491 with the 100-feature model

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3. Prediction from single VCF

Step 1. Create an Input directory

mkdir /home/username/Input_Dir3

Step 2. Store a VCF file generated from variant calling of a MTB isolate based on MTB H37Rv reference genome (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/955/GCF_000195955.2_ASM19595v2/GCF_000195955.2_ASM19595v2_genomic.fna.gz)

Step 3. Create an Output directory

mkdir /home/username/Output_Dir3

Step 4. Go to the mcdr-mtb-standalone-v2 installation directory

cd /home/username/mcdr-mtb-standalone-v2/

Step 5. Run mcdr-VCF-predict.sh

./mcdr-VCF-predict.sh /home/username/Input_Dir3/ /home/username/Output_Dir3/

Input_Dir3 contains ERR137249.vcf

Output_Dir3 contains -

• ERR137249.tsv - the intermediate TSV file
• prediction.tsv - the prediction result performed with the full model
• shap_result_37_features_ERR137249.tsv - the SHAP result for ERR137249 with the 37-feature model
• shap_result_100_features_ERR137249.tsv - the SHAP result for ERR137249 with the 100-feature model
• shap_plot_37_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 37-feature model
• shap_plot_100_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 100-feature model

---

4. Prediction from multiple VCFs

Step 1. Create an Input directory

mkdir /home/username/Input_Dir4

Step 2. Store multiple VCF files generated from variant calling of MTB isolates based on MTB H37Rv reference genome (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/955/GCF_000195955.2_ASM19595v2/GCF_000195955.2_ASM19595v2_genomic.fna.gz)

Step 3. Create an Output directory

mkdir /home/username/Output_Dir4

Step 4. Go to the mcdr-mtb-standalone-v2 installation directory

cd /home/username/mcdr-mtb-standalone-v2/

Step 5. Run mcdr-multi-VCF-predict.sh

./mcdr-multi-VCF-predict.sh /home/username/Input_Dir4/ /home/username/Output_Dir4/

Input_Dir4 contains ERR137249.vcf, SRR1103491.vcf

Output_Dir4 contains -

• Compressed VCFs - ERR137249.vcf.gz and SRR1103491.vcf.gz
• VCF indices - ERR137249.vcf.gz.csi and SRR1103491.vcf.gz.csi
• merged.vcf
• merged.tsv - the intermediate TSV file
• prediction.tsv - the prediction result performed with the full model
• shap_result_37_features_ERR137249.tsv - the SHAP result for ERR137249 with the 37-feature model
• shap_result_100_features_ERR137249.tsv - the SHAP result for ERR137249 with the 100-feature model
• shap_plot_37_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 37-feature model
• shap_plot_100_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 100-feature model
• shap_result_37_features_SRR1103491.tsv - the SHAP result for SRR1103491 with the 37-feature model
• shap_result_100_features_SRR1103491.tsv - the SHAP result for SRR1103491 with the 100-feature model
• shap_plot_37_features_SRR1103491.svg - the SHAP result plot for SRR1103491 with the 37-feature model
• shap_plot_100_features_SRR1103491.svg - the SHAP result plot for SRR1103491 with the 100-feature model

---

5. Prediction from merged VCFs

Step 1. Create an Input directory

mkdir /home/username/Input_Dir5

Step 2. Store a merged VCF file generated by merging multiple VCF files from variant calling of MTB isolates based on MTB H37Rv reference genome (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/955/GCF_000195955.2_ASM19595v2/GCF_000195955.2_ASM19595v2_genomic.fna.gz)

Step 3. Create an Output directory

mkdir /home/username/Output_Dir5

Step 4. Go to the mcdr-mtb-standalone-v2 installation directory

cd /home/username/mcdr-mtb-standalone-v2/

Step 5. Run mcdr-merge-predict.sh

./mcdr-merge-predict.sh /home/username/Input_Dir5/ /home/username/Output_Dir5/

Input_Dir5 contains merged.vcf

Output_Dir5 contains -

• merged.tsv - the intermediate TSV file
• prediction.tsv - the prediction result performed with the full model
• shap_result_37_features_ERR137249.tsv - the SHAP result for ERR137249 with the 37-feature model
• shap_result_100_features_ERR137249.tsv - the SHAP result for ERR137249 with the 100-feature model
• shap_plot_37_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 37-feature model
• shap_plot_100_features_ERR137249.svg - the SHAP result plot for ERR137249 with the 100-feature model
• shap_result_37_features_SRR1103491.tsv - the SHAP result for SRR1103491 with the 37-feature model
• shap_result_100_features_SRR1103491.tsv - the SHAP result for SRR1103491 with the 100-feature model
• shap_plot_37_features_SRR1103491.svg - the SHAP result plot for SRR1103491 with the 37-feature model
• shap_plot_100_features_SRR1103491.svg - the SHAP result plot for SRR1103491 with the 100-feature model

Team

Abhirupa Ghosh, Sudipto Bhattacharjee, and Sudipto Saha

Disclaimer

The scripts were tried and tested on the Ubuntu Operating system.

This tool is strictly for Research Use Only. By using this tool the user acknowledges no intended medical purpose such as patient diagnosis.